ape (version 5.1)

read.gff: Read GFF Files

Description

This function reads a file in general feature format version 3 (GFF3) and returns a data frame.

Usage

read.gff(file, na.strings = c(".", "?"))

Arguments

file

a file name specified by a character string.

na.strings

the strings in the GFF file that will be converted as NA's (missing values).

Value

NULL

Details

The returned data frame has its (column) names correctly set (see References) and the categorical variables (seqid, source, type, strand, and phase) set as factors.

This function should be more efficient than using read.delim.

GFF2 files can also be read but the field names conform to GFF3.

The file can be gz-compressed (see examples), but not zipped.

References

https://en.wikipedia.org/wiki/General_feature_format

Examples

# NOT RUN {
## requires to be connected on Internet
d <- "ftp://ftp.ensembl.org/pub/release-86/gff3/homo_sapiens/"
f <- "Homo_sapiens.GRCh38.86.chromosome.MT.gff3.gz"
download.file(paste0(d, f), "mt_gff3.gz")
gff.mito <- read.gff("mt_gff3.gz")
## the lengths of the sequence features:
gff.mito$end - (gff.mito$start - 1)
table(gff.mito$type)
## where the exons start:
gff.mito$start[gff.mito$type == "exon"]
# }